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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgtagaaaaatattcttctctgtcccctttagctgtattcagtttcatttggcatggctcactgtggcgtctctgggatacataatttggttattcacttccaatgcagGGTCAATTGCTAACTTTGGTTGAATATTTCATGCTTCTGTATCGCTCTTTACTGCCTACCCCTGTATGGTACCGTTTCTTTTTGAACAAGGATTATGGAA

Basic information

species Arabidopsis thaliana
transcript AT5G01960.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G01960.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os05g25180.1 (Oryza sativa), 3'ss of exon 4
gtgatgtagaaaaatattcttctctgtcccctttagctgtattcagtttcatttggcatggctcactgtggcgtctctgggatacataatttggttattcacttccaatgcagGGTCAATTGCTAACTTTGGTTGAATATTTCATGCTTCTGTATCGCTCTTTACTGCCTACCCCTGTATGGTACCGTTTCTTTTTGAACAAGGATTATGGAA
   || | |||   ||   |  |   |    |  | |  | |  |||| ||       | | |   | || |   |||| |   || || ||  |  ||  ||        |||||||| |||||||  | || |||||  |  |||| || |||||  | ||  |||| || ||||| ||||||||||||||| |||||||||| ||||| |
--tatcttgaattctagcttatttcttattttagatccttttatagttgcaagcttagtagttggttctgac--ttctgaggctca-aactttctgttttgct--------agGGTCAAATGCTAACCCTTGTGGAATACCTTCTGCTCCTATATCGTGCCTTGTTGCCAACTCCTGTTTGGTACCGTTTCTTTCTGAACAAGGAATATGGGA

upper sequence: AT5G01960.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0056g00440.t01 (Vitis vinifera), 3'ss of exon 4
gtgatgtagaaaaatattct-tctctgtcccctttagctgtattcagtttcatttggcatggc--tcactgtggcgtctctgggatacataatttggttattcacttccaatgcagGGTCAATTGCTAACTTTGGTTGAATATTTCATGCTTCTGTATCGCTCTTTACTGCCTACCCCTGTATGGTACCGTTTCTTTTTGAACAAGGATTATGGAA
|| | |||  |  | ||| | | |         ||   |    | ||| |||||||   |     ||  | || |  |  |   | ||  | |   |  ||| | || |    ||||||||| ||||||||||||||||||||    | ||  |||||||  | ||  ||||  | ||||| ||||| ||||| || |||||||| || ||||| |
gtaaggtaatatgaaattatgtgttaaagtagatttatttaggttagtatcatttgcatttatattctttttgtctgccattacacactgactccagacatttattttc----cagGGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTGTTGCCAGCACCTGTCTGGTATCGTTTTTTCTTGAACAAAGAATATGGGA
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|164033678|gb|ES054192.1|ES054192
EST:     GTACTACAAAAACAGTAGGGGTCGGAATTATCGTAAACAG                         GGTCAATTGCTAACTTTGGTTGAATATT
genomic: GTACTACAAAAACAGTAGGGGTCGGAATTATCGTAAACAGgtgatgtaga ... tccaatgcagGGTCAATTGCTAACTTTGGTTGAATATT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggctcactgtggcgtctctgggatacataatttggttattcacttccaatgcagGGTCAATTGCTAACTTTGGTTGAATATTTCATGCTTCTGTATCGCTCTTTACTGCCTACCCCTGTATGGTACCGTTTCTTTTTGAACAAGGATTATGGAA
 ggctcac  putative branch site (score: 3)
                                       ttcacttcc  putative PPT
                           ataatttggttatt  TA-rich tract